Locus 690

Sequence ID	2L_DroMel_CAF1
Location	2,009,136 – 2,009,274
Length	138
Max. P	0.900453

overview

Window 6

Location	2,009,136 – 2,009,239
Length	103
Sequences	6
Columns	104
Reading direction	reverse
Mean pairwise identity	82.64
Mean single sequence MFE	-28.67
Consensus MFE	-26.82
Energy contribution	-26.82
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.63
Structure conservation index	0.94
SVM decision value	0.79
SVM RNA-class probability	0.850751
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2009136 103 - 22407834
UUCUUU-GCUUAUCAGGUUCCACCGAGAUUUGAACUCGGAUCGCAGGAUUCAGAGUCCUGAGUGCUAACCAUUACACCAUGGAACCGCUUGUCAAUGAGUCGUC
(((.((-(..((...((((((((((((.......))))).....((.((((((....)))))).)).............)))))))...)).))).)))..... ( -28.00)
>DroPse_CAF1 31259 95 - 1
---------AAAUCAGGUUCCACCGAGAUUUGAACUCGGAUCGCAGGAUUCAGAGUCCUGAGUGCUAACCAUUACACCAUGGAACCAUUUGCGAUGCUGCCGUC
---------......(((..(.(((((.......)))))(((((((.((((((....)))))).))..((((......))))........))))))..)))... ( -28.70)
>DroGri_CAF1 44337 104 - 1
AAGUAAUCGUACUCAGGUUCCACCGAGAUUUGAACUCGGAUCGCAGGAUUCAGAGUCCUGAGUGCUAACCAUUACACCAUGGAACCUCUUACAAAUUGAGUGUC
.........((((((((((((((((((.......))))).....((.((((((....)))))).)).............)))))))..........)))))).. ( -29.70)
>DroMoj_CAF1 17777 104 - 1
AUGCAACUCGAAUCAGGUUCCACCGAGAUUUGAACUCGGAUCGCAGGAUUCAGAGUCCUGAGUGCUAACCAUUACACCAUGGAACCACCAAUGAAUUUUCUGUC
...............((((((((((((.......))))).....((.((((((....)))))).)).............))))))).................. ( -26.90)
>DroAna_CAF1 23987 102 - 1
A-CUUA-UUCGAUCAGGUUCCACCGAGAUUUGAACUCGGAUCGCAGGAUUCAGAGUCCUGAGUGCUAACCAUUACACCAUGGAACCGAAUGUCUUUCUGGCGUC
.-....-........((((((((((((.......))))).....((.((((((....)))))).)).............)))))))..(((((.....))))). ( -30.00)
>DroPer_CAF1 30111 95 - 1
---------AAUUCAGGUUCCACCGAGAUUUGAACUCGGAUCGCAGGAUUCAGAGUCCUGAGUGCUAACCAUUACACCAUGGAACCAUUUGCGAUGCUGCCGUC
---------......(((..(.(((((.......)))))(((((((.((((((....)))))).))..((((......))))........))))))..)))... ( -28.70)
>consensus
A__U_A___AAAUCAGGUUCCACCGAGAUUUGAACUCGGAUCGCAGGAUUCAGAGUCCUGAGUGCUAACCAUUACACCAUGGAACCACUUGCGAAUCUGCCGUC
...............((((((((((((.......))))).....((.((((((....)))))).)).............))))))).................. (-26.82 = -26.82 +  -0.00)

alignment

secondary structure

dotplot

Window 7

Location	2,009,176 – 2,009,274
Length	98
Sequences	4
Columns	100
Reading direction	reverse
Mean pairwise identity	72.57
Mean single sequence MFE	-18.24
Consensus MFE	-15.61
Energy contribution	-16.30
Covariance contribution	0.69
Combinations/Pair	1.06
Mean z-score	-1.05
Structure conservation index	0.86
SVM decision value	1.01
SVM RNA-class probability	0.900453
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2009176 98 - 22407834
UGUAUUGAACAAAAUAA-AAAUAAAUAACAAAAAAGUUCUUU-GCUUAUCAGGUUCCACCGAGAUUUGAACUCGGAUCGCAGGAUUCAGAGUCCUGAGUG
.(((..((((.......-.................))))..)-))...((((((((..(((((.......)))))(((....)))...))).)))))... ( -19.26)
>DroPse_CAF1 31299 77 - 1
UAUA---AA--AAAUAC-C-----GU---AAAGCAG---------AAAUCAGGUUCCACCGAGAUUUGAACUCGGAUCGCAGGAUUCAGAGUCCUGAGUG
....---..--.....(-(-----(.---....(((---------(..((.((.....))))..))))....)))....((((((.....)))))).... ( -16.90)
>DroGri_CAF1 44377 90 - 1
----UUUAAA-AAGUUCUAAAUAAAU---GAAAA--AAGUAAUCGUACUCAGGUUCCACCGAGAUUUGAACUCGGAUCGCAGGAUUCAGAGUCCUGAGUG
----......-...............---.....--.........(((((((((((..(((((.......)))))(((....)))...))).)))))))) ( -19.50)
>DroPer_CAF1 30151 77 - 1
UAUA---AA--AAAUAC-C-----GU---AAAGCAG---------AAUUCAGGUUCCACCGAGAUUUGAACUCGGAUCGCAGGAUUCAGAGUCCUGAGUG
....---..--.....(-(-----(.---....(((---------(.(((.((.....))))).))))....)))....((((((.....)))))).... ( -17.30)
>consensus
UAUA___AA__AAAUAC_A_____AU___AAAAAAG_________AAAUCAGGUUCCACCGAGAUUUGAACUCGGAUCGCAGGAUUCAGAGUCCUGAGUG
..............................................((((((((((..(((((.......)))))(((....)))...))).))))))). (-15.61 = -16.30 +   0.69)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:42:58 2006